I like a lot of the episodes but the one that sticks out is probably Holy Matrimony. xD I'm such a Rocketshipper, and the end made me so happy! Plus I love James and seeing his background was awesome. (I didn't remember him being from a rich family or having a fiancee from when I was little... must have missed that epi.)
Pokemon Shipwreck is another. Again, probably because of the Rocketshippy stuff in it. xD Plus I always love episodes where Team Rocket and the twerps have to work together. (Forest Grumps is another one! They work together and I love it. :P)
Ghost of Maiden's Peak, Tower of Terror, and any episode that focuses on TR more than Ash and Co.
I sometimes watch subbed Japanese episodes too before the dubbed one comes out. I loved Kojiro's Treasure Chest, sort of like the sequel to Holy Matrimony. :D
*put way too much thought into this post*